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Use of the ptxD gene as a portable selectable marker for chloroplast


transformation in Chlamydomonas reinhardtii

Article  in  Molecular Biotechnology · June 2019


DOI: 10.1007/s12033-019-00177-3

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Molecular Biotechnology
https://doi.org/10.1007/s12033-019-00177-3

ORIGINAL PAPER

Use of the ptxD gene as a portable selectable marker for chloroplast


transformation in Chlamydomonas reinhardtii
José M. Sandoval‑Vargas1 · Luis A. Jiménez‑Clemente1 · Karla S. Macedo‑Osorio1 · María C. Oliver‑Salvador1 ·
Luis C. Fernández‑Linares1 · Noé V. Durán‑Figueroa1 · Jesús A. Badillo‑Corona1

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Abstract
Synthetic biology and genetic engineering in algae offer an unprecedented opportunity to develop species with traits that
can help solve the problems associated with food and energy supply in the 21st century. In the green alga Chlamydomonas
reinhardtii, foreign genes can be expressed from the chloroplast genome for molecular farming and metabolic engineering
to obtain commodities and high-value molecules. To introduce these genes, selectable markers, which rely mostly on the use
of antibiotics, are needed. This has risen social concern associated with the potential risk of horizontal gene transfer across
life kingdoms, which has led to a quest for antibiotic-free selectable markers. Phosphorus (P) is a scarce nutrient element
that most organisms can only assimilate in its most oxidized form as phosphate (Pi); however, some organisms are able to
oxidize phosphite (Phi) to Pi prior to incorporation into the central metabolism of P. As an alternative to the use of the two
positive selectable makers already available for chloroplast transformation in C. reinhardtii, the aadA and the aphA-6 genes,
that require the use of antibiotics, we investigated if a phosphite-based selection method could be used for the direct recovery
of chloroplast transformed lines in this alga. Here we show that following bombardment with a vector carrying the ptxD
gene from Pseudomonas stutzeri WM88, only cells that integrate and express the gene proliferate and form colonies using
Phi as the sole P source. Our results demonstrate that a selectable marker based on the assimilation of Phi can be used for
chloroplasts transformation in a biotechnologically relevant organism. The portable selectable marker we have developed
is, in more than 18 years, the latest addition to the markers available for selection of chloroplast transformed cells in C.
reinhardtii. The ptxD gene will contribute to the repertoire of tools available for synthetic biology and genetic engineering
in the chloroplast of C. reinhardtii.

Keywords  Phosphite assimilation · Chlamydomonas reinhardtii · ptxD · Selectable marker · Chloroplast transformation

Introduction C. reinhardtii has the potential to serve as the chassis for


sustainable synthetic biology [4] to broaden the availability
Algae are photosynthetic eukaryotic organisms that natu- and diversity of natural products, including enzymes, fatty
rally produce a wide range of metabolites such as pigments, acids, pigments, vitamins, antibodies, therapeutic-drugs,
lipids and polysaccharides. One in particular, the unicellular food additives, polysaccharides, polymers and biomass.
green alga Chlamydomonas reinhardtii, has served both as Engineering of the nuclear and chloroplast genomes is pos-
a model organism to study photosynthesis, phototropism, sible in C. reinhardtii, but the latter is the technology, known
flagellar function and cell cycle control and as a platform as transplastomic technology, that has emerged as promising
to explore production of recombinant proteins, terpenoids alternative to overcome many of the drawbacks associated
and hydrogen and lipids for biofuels [1–3]. Furthermore, with nuclear transformation.
For the last two decades, transplastomic technology in C.
reinhardtii has been mostly used to demonstrate that high-
* Jesús A. Badillo‑Corona
jbadilloc@ipn.mx value and complex compounds such as antibodies, therapeu-
tic proteins and vaccines can be produced at economically
1
Instituto Politécnico Nacional, Unidad Profesional feasible levels [5, 6]. More recently, efforts have turned to
Interdisciplinaria de Biotecnología, Av. Acueducto SN, Col. explore the feasibility of using this alga as a platform for
Barrio la Laguna Ticomán, 07340 Mexico City, Mexico

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the production of commodities that could be used to address phosphite assimilation [25]. The ptxD gene, from the ptxAB-
the demand of biofuels [3, 7]. The chloroplast of C. rein- CDE operon from Pseudomonas stutzeri WM 88, encodes a
hardtii contains ~ 80 copies of a 205-kb genome compris- NAD-dependent phosphite dehydrogenase, which catalyzes
ing each over 100 genes coding for proteins and RNAs that the oxidation of Phi to Pi with the concomitant reduction
are involved in photosynthesis and plastid transcription and of ­NAD+ to NADH [26]. Following stable integration and
translation [8, 9]. To achieve chloroplast transformation, expression of the ptxD gene, strains of C. reinhardtii were
selectable marker genes are essential tools for efficient iden- able to assimilate phosphite and use it as the sole phospho-
tification of transformed strains. Chloroplast transformation rus source. However, in our previous work we had to select
was first achieved in C. reinhardtii by restoring photosyn- transformed lines based on their ability to tolerate the pres-
thesis following introduction of the wild-type aptB gene into ence of the antibiotic spectinomycin, as the transformation
mutant strains carrying deletions or point mutations in this of chloroplasts was carried out in combination with vec-
gene [10]. Since then, use of the corresponding wild-type tor p228 (Chlamydomonas Resource Center, University
gene to restore photosynthesis in recipient lines carrying of Minnesota) which carries a dominant point mutation
large deletions, frameshift mutations or non-sense deletions (spr-u-1-6-2) in the 16S rRNA gene [27]. This had to be
in the psbA [11], psaB [12], tscA [13], atpE [14] and rbcL done because we did not know if transformed lines could be
[15] genes has been successfully demonstrated. However, directly selected based on their ability to metabolize phos-
these approaches have relied on the use of existing mutant phite. Here we investigated if the ptxD gene could be used
from forward genetic screenings. More recently, the group directly, without the use of genes that confer resistance to
of Saul Purton have developed a strain in which the psbH antibiotics, as a selectable marker to carry out chloroplast
gene has been disrupted with an expression cassette for the transformation in C. reinhardtii. We are showing that trans-
aadA gene [16, 17]. This photosynthetic deficient strain can- formed cells develop into visible colonies when growing in
not grow in the absence of acetate. Transformation in this media containing phosphite as the sole phosphorus source
strain can be then accomplished with the use of a vector car- with no false positive colonies. Use of the ptxD gene as
rying the gene of interest and a functional psbH gene [18]. selectable marker for nuclear transformation of C. rein-
After recombination, the aadA gene is eliminated yielding hardtii has already been demonstrated, but this is the first
photosynthetically competent and aadA-free cells. This time that this gene has been used as selectable marker for
marker-free approach has been used to express the PfCel- chloroplast transformation in this photosynthetic organism.
TOS antigen from P. falciparum to develop an ELISA test Furthermore, we are demonstrating that phosphite-assimi-
for diagnosis of malaria [19] and the fusion protein con- lating strains can endure relaxed conditions of media and
sisting of the PfCelTOS antigen and human interleukin-2 photobioreactor preparation with no apparent contamination
(PfCelTOS:IL-2), a vaccine candidate fused to human inter- during a 15-day cultivation time-course.
leukin-2 (IL-2) as vaccine adjuvant [20].
In contrast to the more diverse options available for chlo-
roplast transformation in plants [21–23], chloroplast trans- Materials and Methods
formation in C. reinhardtii currently counts with just two
portable selectable markers, that is, transgenes that coupled Algal Strain and Culture Conditions
with endogenous cis transcription and translation elements
can be used for direct recovery of transformed lines based The wild-type C. reinhardtii CC-125 (mt +) strain (Cr-wt)
on a phenotypic trait. These dominant antibiotic resist- was obtained from the Chlamydomonas Resource Center
ance markers are: the aadA gene [13], encoding an ami- (Chlamydomonas Resource Center, University of Min-
noglycoside 3″-adenylyltransferase conferring resistance nesota, USA) and grown in standard TAP medium [28].
to spectinomycin, and the aphA-6 gene [24], encoding an Additionally, four media, termed TA, TAPhi, TP and TPhi,
aminoglycoside 3′-phosphotransferase conferring resistance were used at the same pH and molar concentrations of com-
to kanamycin. These markers have been used extensively ponents as in the TAP formulation. TA medium contains
with a low, but relevant, false positives rate; up to 10% for no phosphorus source; TAPhi medium contains monobasic
the aphA-6 gene [24]. Given the concerns of using genes potassium phosphite (­ KH2PO3; Wanjie International, China),
that confer resistance to antibiotics and the strict regulatory whereas TP and TPhi media contain no acetate as carbon
requirements for the commercialization of genetically modi- source and contain phosphate and phosphite as phosphorus
fied organisms and their products, development of efficient, source, respectively. For solid cultures, 1.5% (w/v) of agar
portable selectable markers that can spare the use of antibi- was used. Solid cultures were maintained under illumination
otics is highly needed. at 50 µmol photons ­m−2 s−1 of white LED light, in a 16:8 h
Recently, we have shown that the ptxD gene can be (light/dark) photoperiod at 25 °C while sterile liquid cultures
used to engineer the chloroplast of C. reinhardtii to enable were grown under the same conditions but with constant

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Molecular Biotechnology

agitation at 150 rpm in an orbital shaker. For P-starved gel electrophoresis (1% agarose) using Gel Red DNA Gel
cultures, cells at late mid-log phase in TAP medium were Stain (Biotium Inc, USA).
harvested and washed twice with TA medium. A total of
1 × 108 cells were transferred to liquid TA medium for 7 or Immunodetection of PTXD
14 days with agitation in an orbital shaker at 150 rpm and
under the same culture conditions as described above. After Total soluble protein (TSP) extraction was carried out
each starvation period, cells were harvested, washed twice according to [11]. TSP was quantified by Bradford assay
with TA medium, and re-suspended in TA to reach a final with Quick Start Bradford 1 × Dye Reagent (Bio-Rad) fol-
concentration of 1 × 105 cells. lowing the manufacturer’s instructions and using bovine
Bottles (1 L) containing 800 mL of non-sterile TP, for serum albumin as a standard for a calibration curve of known
the wild-type strain, and 800 mL of non-sterile TPhi, for amounts. A total of 30 μg of TSP were separated by electro-
transplastomic strains, were inoculated with 1­ x105 TAP- phoresis in a 12% polyacrylamide gel with denaturing condi-
grown cells, placed in a 12:12 h (light–dark) photoperiod tions and then transferred to Immun-Blot PVDF Membranes
at 24° C under 180 μmol photons m ­ −2 s−1 of white light and (Bio-Rad) as described by [31]. Membranes were probed
air-bubbled at 0.4–0.5 vvm. The algal growth was estimated with a horseradish peroxidase conjugated mouse monoclonal
every 24 h by measuring the optical density at 750 nm and antibody to the DDDDK epitope present in the 3X-FLAG
by direct cell counting using a hemocytometer. tag at the N-terminal of PTXD (Abcam, United Kingdom).
The membrane was developed with Western Lightning Plus-
ECL reagent (Perkin Elmer Inc., Netherlands) and recorded
Chloroplast Transformation
using a Chemi DOC MP Imaging system (Bio Rad).
Chloroplast transformation was carried out by particle bom-
Southern Blotting
bardment using p320-PpsbD-ptxD according to the meth-
odology described in [29] with slight modifications. Prior
For Southern blotting, total DNA from wild-type and
to bombardment, 7-days or 14-days P-starved wild-type C.
transplastomic C. reinhardtii was isolated using the Wiz-
reinhardtii cells were plated over solid 5 mM TAPhi media
ard Genomic DNA Purification Kit (Promega, USA) fol-
and placed under sterile conditions in a dark room for 2 h
lowing the manufacturer’s instructions for plant extraction.
to air-dry the excess of liquid medium. Plated cells were
For DNA preparation, total DNA lines were digested with
subjected to particle bombardment with the Biolistic PDS-
endonucleases EcoRI and XhoI (Thermo Fisher Scientific,
1000/He Particle Delivery System (Bio Rad) at 9 cm of dis-
USA). Fragments were separated by electrophoresis in a
tance using 1100 psi rupture disks (Bio Rad) and 30 in Hg
0.8% agarose gel, and DNA was transferred to a Zeta-probe
vacuum pressure within the chamber. After bombardment,
nylon membrane (Bio Rad) by alkaline blotting following
plates were maintained in the dark for 3 days before being
the manufacturer’s instructions or according to [32]. Mem-
transferred to an incubation chamber at 25 °C with a 16:8 h
branes were hybridized with a DNA probe for the ptxD gene
light/dark photoperiod for > 7 weeks. TAPhi-resistant colo-
(~ 1100 bp), which was amplified by PCR using the specific
nies were selected among the green lawn and transferred
primers (JAB489 and JAB490) and labeled with [α-32P]
to freshly prepared TAPhi plates and sub-cultivated for
dATP by random priming according to [33]. The membrane
1–2 weeks.
was hybridized and exposed to a phosphor imaging screen
(Bio Rad) for 1–2 h. Screens were scanned using a Personal
Molecular Characterization Molecular Imager PMI (Bio Rad). The analysis of the image
obtained was done using the Quantity One 1-D Analysis
DNA extraction from wild-type and transplastomic lines was Software (Bio Rad).
carried out using the resin Chelex-100 (Bio-Rad) follow-
ing a previously reported method [29, 30]. PCR was carried
out using PCR 2 × Master mix (Thermo- Scientific, USA) Results and Discussion
following the manufacturer’s instructions using JAB489
(5′-ATG​GAC​TAT​AAG​GAT​CAC​GA-3′) and JAB490 (5′- To investigate if the ptxD gene can be directly used as a
TTA​GCA​GGC​GGC​GGG​CTC​CG-3´) primers to amplify selectable marker for chloroplast transformation in C. rein-
the ~ 1100 bp product corresponding to the ptxD gene, and hardtii, we used vector p320-PpsbD-ptxD. In this vector,
primers LCT 59 (5′-CGTG ​ GAG​ TAT
​ TTA​ ATA​ CAG
​ CTA-3′) the ptxD from P. stutzeri WM88 is under the control of the
and LCT 68 (5′-CCC​ATA​AAT​AGT​TTC​AAT​TGGA-3′) to psbD promoter and the rbcL terminator. The ptxD gene
amplify the 2174-bp product corresponding to the PpsbD- was optimized for C. reinhardtii chloroplast codon usage
ptxD-TrbcL cassette. The PCR products were analyzed by (Genbank MG823244) and contains the sequence coding

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for a modified 3X-FLAG at the 5´-end. Flanking sequences Phi does not support growth but is not toxic to algae, thus
target the insertion of the expression cassette to the region allowing cells to remain viable using internal Pi reserves
in the inverted repeat of the chloroplast genome between [34]. We then reasoned that a stringent selective pressure
23S-5S rRNA/exon5-intron 4 of psbA (Fig. 1a). As a first could favor the proliferation of ptxD transformed lines.
approach, we followed the transformation protocol we To do this, we cultivated wild-type cells in P-depleted
routinely use for chloroplast transformation using tung- TAP media (termed here TA media) for 7-days with the
sten particle bombardment. Cells grown in TAP medium aim of starving the cells for P and force them to consume
were placed as a lawn on TAPhi medium, instead of the endogenous Pi reserves. Upon introduction of the ptxD
antibiotic-supplemented TAP medium, normally used for gene, we thought, transformed cells would rapidly pro-
selection when the aadA or the aphA-6 genes are used liferate whilst the starved cells would continue to die.
[29]. Following bombardment, we could not recover Phi- P-starved cells were used for transformation with vector
assimilating colonies; in fact, we continued to observe a p320-PpsbD-ptxD. After about 50 days, we observed the
grainy slightly pale green lawn of algae even after more proliferation of a single colony growing in TAPhi media,
than 60 days in TAPhi media (Fig. 1b; event 1). This is presumably using Phi as P source. When the colony was
not entirely surprising, as it has been demonstrated that about 5 mm (60 days post-bombardment), we transferred it

Fig. 1  Generation of transplastomic, phosphite-assimilating lines of cells (Event 2). c Molecular characterization of the only phosphite
C. reinhardtii using the ptxD gene as a selectable maker. a C. rein- assimilating line Crc-PhiX obtained from bombardment of a 7-day
hardtii wild-type genome targeted for insertion of the ptxD gene P-depleted culture. From top to bottom: PCR amplification of the
and chloroplast transformation vector p320-PpsbD-ptxD. Expres- ptxD gene, RFLP analysis using a specific [α-32P] dATP labeled
sion of ptxD gene is regulated by psbD promoter and rbcL termi- probe specific for the full length ptxD coding sequence, immunode-
nator, this expression cassette is flanked by homologous recom- tection of the PTXD protein using an anti-3XFLAG monoclonal anti-
bination sequence of 23S-5S rRNA and exon 5-intron 4 of psbA. b body and SDS-PAGE stained with Coomassie brilliant blue to verify
Particle bombardment of P-replete (Event 1) and 7-day P-depleted equal amount of protein loading

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Molecular Biotechnology

to fresh TAPhi media (using a wild-type strain as a nega- Crc-Phi1, confirming that the ptxD can be directly used as
tive control) and allowed it to proliferate for a few days a portable selectable marker for chloroplast transformation
(Fig. 1b; event 2). We termed this line Crc-PhiX (Chla- in C. reinhardtii.
mydomonas reinhardtii chloroplast phosphite assimilating Next, we tried to increase the transformation efficiency of
strain X) and carried out a full molecular characterization. one Phi-assimilating colony per bombardment. We investi-
We found that the expression cassette had integrated in gated if an increase on the P-starvation period could have a
the chloroplast genome in the expected locus and detected positive effect on the number of transformed lines recovered.
the presence of the ptxD transcript and the 39-kDa PTXD To do this, we used 14-day P-starved cells and followed the
protein (Fig. 1c). We used one of our previously reported same transformation protocol as described before. We found
Phi-assimilating strains Crc-Phi1 [25] and showed that, at that this time a greater number of colonies proliferated on
the molecular level, Crc-PhiX was indistinguishable from TAPhi media and were fully visible by day 30 (Fig. 2a).

Fig. 2  Optimization of the efficiency on the use of the ptxD gene type line to demonstrate homoplasmy. c Summary of transformation
as a selectable marker for chloroplast transformation and growth of events, P-starvation regime and transformation efficiencies. d Wild-
phosphite-assimilating strains under non-sterile conditions. a Parti- type strain in TP medium and phosphite-assimilating transplastomic
cle bombardment of 14-day P-depleted cells (Events 3 and 4). b PCR strains of C. reinhardtii, Crc-PhiX and Crc-Phi1, growing in non-ster-
amplification of the ptxD gene in lines obtained in Events 3 and 4. ile photo- and mix-autotrophic conditions in TPhi and TAPhi media,
PCR amplification of the 2174-bp PpsbD-ptxD-TrbcL cassette in respectively. e Growth kinetics of transplastomic Crc-PhiX and Crc-
selected transplastomic lines and the 202-bp fragment in the wild- Phi1 lines growing in photo- and mix-autotrophic conditions

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Molecular Biotechnology

We carried out this experiment in duplicate and obtained an under photoautotrophic conditions in loosely prepared 1 L
average of 22 Phi-assimilating colonies (Fig. 2a), a consider- cultures. Bottles containing non-sterile TPhi media were
able improvement from the one colony obtained with 7-day inoculated with 1­ x105 TAP-grown cells, placed in a 12-h
P-starved cells (Fig. 2c). All colonies were used to deter- light/12-h dark photoperiod under 180 μmol photons/m2·s
mine the presence of the ptxD gene using specific primers and air-bubbled at 0.4–0.5 vvm without the use of air fil-
to amplify the 1100-bp ptxD gene. In all transformed lines, ters (Fig. 2d). We measured the cell density daily and made
but not in the wild-type strain, we successfully amplified a observations under the microscope to follow the evolution
fragment of the expected size (Fig. 2b, top two panels), indi- of the culture. Both Crc-Phi1 and Crc-PhiX growing in
cating that the ptxD gene was present in the lines obtained TPhi media remained without noticeable contamination up
and thus indirectly demonstrating that the Phi-assimilating to 15 days after the start of the culture and reaching a cell
phenotype was the result of the biologically active PTXD density of ~ 1.6 × 106 cell/mL (Fig. 2e, TPhi-CrcPhiX and
protein, catalyzing the oxidation of Phi to metabolizable TPhi-Crc-Phi1) similar to a wild-type strain growing in TAP
Pi. Notably, no false positives were detected, a drawback media under sterile conditions (not shown). By contrast, the
frequently observed when the aadA [13] and aphA-6 genes culture inoculated with the wild-type strain, growing in TP
are used as selectable markers [24]. In all 11 lines obtained media, was overgrown by invading species by day 7 (Fig. 2d,
in event 3, we determined homoplasmy by amplifying the TP-Wild-type; Fig. 2e, TP-Cr-Wt). Similarly, the Crc-PhiX
PpsbD-ptxD-TrbcL cassette using primers laying outside of strain, growing in TAPhi media was also overgrown by uni-
the BamHI and SpeI site in the wild-type and transformed dentified invading species of bacteria and fungi revealed
genome (Fig. 1a). We amplified the expected fragments of by observations we made under the microscope (Fig. 2d,
202 bp and 2174 bp for the wild-type and transplastomic TAPhi-Crc-PhiX). We did not follow-up to identify the
lines, respectively. We did not get amplification of the 202- invading species as it falls out of the scope of this study.
bp fragment in the transformed lines, indicating that lines Our results show that transplastomic strains of C. reinhardtii
were homoplasmic and that the wild-type genome was no expressing the ptxD gene can be grown under non-sterile
longer present. Figure 2c shows a summary of the results of condition, keeping species that are uncapable of assimilating
the transformation events we have described above. The effi- phosphite at bay. Furthermore, we have kept lines Crc-Phi1
ciency of transformation we have obtained (1-50 colonies) is and Crc-PhiX for 2 years and 6 months, respectively, grow-
in the range of what is normally observed for other selecta- ing in phosphite as the sole phosphorus source and have not
ble markers, 5-100 transformed colonies for aphA-6 [24] detected signs of the ptxD gene being unstable.
and 8-50 for 16S rRNA carrying a dominant point mutation Our result is highly relevant as it opens the possibility
[35]. Other groups have used the ptxD gene as a portable to use chloroplast transformed strains of a generally rec-
selectable marker, albeit for transformation of the nuclear ognized as safe (GRAS) organism for the production of
genome, in yeasts [36] and in plants including tobacco and biotechnologically, perhaps non-health-related, compounds
Arabidopsis [37], maize [38], cotton [39] and sorghum [40]. in laxly prepared semi-closed bioreactors or open raceway
To the best of our knowledge, this is the first time that the reactors. These type of cultures would keep the overall pro-
ptxD gene has been used as a portable selectable marker for duction cost low, as the requirement for the sterilization of
chloroplast transformation in C. reinhardtii, allowing direct upstream unitary operations could be eliminated. Phosphite
selection of transplastomic cells which are able to use phos- assimilating cultures producing industrially relevant metabo-
phite as the phosphorus source. lites could be kept for longer thus increasing the productiv-
Engineering phosphite metabolism in algae, and per- ity while lowering the cost of the final product. Recently
haps other organisms, represents an invaluable tool for the cyanobacteria have been engineered to rely exclusively on
management of biological contaminants in closed and open the assimilation of phosphite for growth [42], as opposed to
cultures [41] and to develop synthetic organisms that can be our strains, which can also use phosphate, suggesting that a
self-contained [42]. Using nuclear transformed algae Loera- similar strategy could be applied to an eukaryotic alga such
Quezada et al. [41] have demonstrated that when cultivated as C. reinhardtii in the future.
in bioreactors prepared with non-sterile water and chemicals,
Phi-assimilating strains can colonize a non-sterile environ-
ment where phosphite is the only source of phosphorus. Conclusions
Furthermore, these strains can outcompete other species of
algae uncapable of assimilating Phi. Using one of our pre- Here we have shown that the ptxD gene can be used as a
viously obtained transplastomic strains, Crc-Phi1 [25] and selectable marker for chloroplast transformation in Chla-
Crc-PhiX (this work), we investigated if these lines, express- mydomonas reinhardtii allowing easy visual selection of
ing the ptxD gene from the chloroplast genome, showed a phosphite-assimilating colonies without the need of antibi-
similar behavior to those reported by [41] when growing otics. Furthermore, we have shown that the transformation

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efficiency increases when 14-day P-starved cells are used reinhardtii. Journal of Biotechnology, 195, 60–66. https​://doi.
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